dbSNP rs941389: UGT2B4:c.44-613T>G (chr4-69496023-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001297616.2(UGT2B4):c.44-613T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 1,237,918 control chromosomes in the GnomAD database, including 80,331 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 8720 hom., cov: 32)

Exomes 𝑓: 0.36 ( 71611 hom. )

Consequence

UGT2B4
NM_001297616.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.414

Variant links:

Genes affected

UGT2B4 (HGNC:12553): (UDP glucuronosyltransferase family 2 member B4) Enables glucuronosyltransferase activity. Involved in cellular glucuronidation and estrogen metabolic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

UGT2B4 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
UGT2B4	NM_001297616.2 link	c.44-613T>G	intron_variant	Intron 1 of 6		NP_001284545.1	P06133-2
UGT2B4	NM_021139.3 link	c.-162T>G	upstream_gene_variant		ENST00000305107.7	NP_066962.2	P06133-1
UGT2B4	NM_001297615.2 link	c.-162T>G	upstream_gene_variant			NP_001284544.1	P06133-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B4	ENST00000305107.7 link	c.-162T>G		upstream_gene_variant		1	NM_021139.3	ENSP00000305221.6		P06133-1

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

51159

AN:

151888

Hom.:

8724

Cov.:

show subpopulations

Gnomad AFR

AF:

0.296

Gnomad AMI

AF:

0.338

Gnomad AMR

AF:

0.311

Gnomad ASJ

AF:

0.345

Gnomad EAS

AF:

0.258

Gnomad SAS

AF:

0.363

Gnomad FIN

AF:

0.324

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.373

Gnomad OTH

AF:

0.340

GnomAD4 exome

AF:

0.359

AC:

390201

AN:

1085912

Hom.:

71611

AF XY:

0.359

AC XY:

191799

AN XY:

533812

show subpopulations

Gnomad4 AFR exome

AF:

0.298

Gnomad4 AMR exome

AF:

0.291

Gnomad4 ASJ exome

AF:

0.342

Gnomad4 EAS exome

AF:

0.221

Gnomad4 SAS exome

AF:

0.365

Gnomad4 FIN exome

AF:

0.320

Gnomad4 NFE exome

AF:

0.370

Gnomad4 OTH exome

AF:

0.349

GnomAD4 genome

AF:

0.337

AC:

51175

AN:

152006

Hom.:

8720

Cov.:

AF XY:

0.332

AC XY:

24680

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.295

Gnomad4 AMR

AF:

0.311

Gnomad4 ASJ

AF:

0.345

Gnomad4 EAS

AF:

0.258

Gnomad4 SAS

AF:

0.362

Gnomad4 FIN

AF:

0.324

Gnomad4 NFE

AF:

0.373

Gnomad4 OTH

AF:

0.340

Alfa

AF:

0.359

Hom.:

1559

Bravo

AF:

0.333

Asia WGS

AF:

0.314

AC:

1085

AN:

3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.23

DANN

Benign

0.39

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over